I'm glad you got it working, but I'd asked WD's engineers about that in the past...
The answer I got was that because the USB controller handles any "translations" and acts as a go-between, that Microsoft is incorrect on their pages to say that you can't use GPT and/or 4K sectors over USB, and that WD's large drives work with all (supported) versions of Windows.
Other Microsoft pages certainly say that you can ONLY use MBR over USB with Windows XP (regardless of physical sector size), and that certainly does NOT seem to be the case. In that case, WD seems quite correct in their assertion that GPT drives work over USB with XP... it's only internally that XP can't use GPT.
So, since the USB controller "hides" the GPT and lets a USB drive be accessed by an OS that simply doesn't support GPT, and since WD's Advanced Format drives emulate 512-byte sectors anyways, even if there wasn't the USB controller in-between acting as interpreter, it seems unlikely to me that 4096-byte sectors (emulated) over USB are unsupported by Windows XP, as Microsoft claims. According to that article from Microsoft that you linked, pretty much NONE of WD's USB drives should work under Windows XP, and the current user base seems to repudiate that.
And, the article you linked says that Advanced Format drives _ ARE _ supported under Vista and Windows 7, so the Advanced Format drive in your 3TB should be supported, and the 4096-byte sectors shouldn't have been the root of your problems.